Using answer set programming to deal with Boolean networks and attractor computation: application to gene regulatory networks of cells

DOI10.1007/s10472-023-09886-7MaRDI QIDQ6059225

Van-Giang Trinh, Belaïd Benhamou, Tarek Khaled

Publication date: 2 November 2023

Published in: Annals of Mathematics and Artificial Intelligence (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s10472-023-09886-7

zbMATH Keywords

attractor; logic programming; systems biology; answer set programming; Boolean network; gene regulatory network; cellular phenotype

Mathematics Subject Classification ID

68-XX: Computer science

Cites Work

• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• An efficient approach of attractor calculation for large-scale Boolean gene regulatory networks
• ASSAT: computing answer sets of a logic program by SAT solvers
• Hypothesizing about signaling networks
• Extending and implementing the stable model semantics
• P\(_-\)UNSAT approach of attractor calculation for Boolean gene regulatory networks
• The \textit{Arabidopsis thaliana} flower organ specification gene regulatory network determines a robust differentiation process
• The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model
• The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in \textit{Drosophila melanogaster}
• Detecting inconsistencies in large biological networks with answer set programming
• Multi-shot ASP solving with clingo
• Conflict-Driven Answer Set Enumeration
• A machine program for theorem-proving